Job ID = 5720244 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 22,972,055 reads read : 22,972,055 reads written : 22,972,055 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR9972840.sra.cache’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:04:48 22972055 reads; of these: 22972055 (100.00%) were unpaired; of these: 2025457 (8.82%) aligned 0 times 18240975 (79.41%) aligned exactly 1 time 2705623 (11.78%) aligned >1 times 91.18% overall alignment rate Time searching: 00:04:48 Overall time: 00:04:48 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 6794667 / 20946598 = 0.3244 in library ' ' BAM に変換しました。 Bed ファイルを作成中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:49:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 15 Apr 2020 22:49:45: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:49:45: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:49:50: 1000000 INFO @ Wed, 15 Apr 2020 22:49:55: 2000000 INFO @ Wed, 15 Apr 2020 22:50:00: 3000000 INFO @ Wed, 15 Apr 2020 22:50:04: 4000000 INFO @ Wed, 15 Apr 2020 22:50:09: 5000000 INFO @ Wed, 15 Apr 2020 22:50:14: 6000000 WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:50:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 15 Apr 2020 22:50:15: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:50:15: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:50:18: 7000000 INFO @ Wed, 15 Apr 2020 22:50:20: 1000000 INFO @ Wed, 15 Apr 2020 22:50:23: 8000000 INFO @ Wed, 15 Apr 2020 22:50:25: 2000000 INFO @ Wed, 15 Apr 2020 22:50:28: 9000000 INFO @ Wed, 15 Apr 2020 22:50:30: 3000000 INFO @ Wed, 15 Apr 2020 22:50:32: 10000000 INFO @ Wed, 15 Apr 2020 22:50:34: 4000000 INFO @ Wed, 15 Apr 2020 22:50:37: 11000000 INFO @ Wed, 15 Apr 2020 22:50:39: 5000000 INFO @ Wed, 15 Apr 2020 22:50:42: 12000000 INFO @ Wed, 15 Apr 2020 22:50:44: 6000000 BedGraph に変換中... WARNING: Skipping mount /opt/pkg/singularity/3.5.2/var/singularity/mnt/session/etc/resolv.conf [files]: /etc/resolv.conf doesn't exist in container INFO @ Wed, 15 Apr 2020 22:50:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.bam'] # control file = None # effective genome size = 9.00e+07 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 15 Apr 2020 22:50:45: #1 read tag files... INFO @ Wed, 15 Apr 2020 22:50:45: #1 read treatment tags... INFO @ Wed, 15 Apr 2020 22:50:46: 13000000 INFO @ Wed, 15 Apr 2020 22:50:48: 7000000 INFO @ Wed, 15 Apr 2020 22:50:50: 1000000 INFO @ Wed, 15 Apr 2020 22:50:51: 14000000 INFO @ Wed, 15 Apr 2020 22:50:52: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:50:52: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:50:52: #1 total tags in treatment: 14151931 INFO @ Wed, 15 Apr 2020 22:50:52: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:50:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:50:52: #1 tags after filtering in treatment: 14151931 INFO @ Wed, 15 Apr 2020 22:50:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:50:52: #1 finished! INFO @ Wed, 15 Apr 2020 22:50:52: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:50:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:50:53: #2 number of paired peaks: 1837 INFO @ Wed, 15 Apr 2020 22:50:53: start model_add_line... INFO @ Wed, 15 Apr 2020 22:50:53: 8000000 INFO @ Wed, 15 Apr 2020 22:50:53: start X-correlation... INFO @ Wed, 15 Apr 2020 22:50:53: end of X-cor INFO @ Wed, 15 Apr 2020 22:50:53: #2 finished! INFO @ Wed, 15 Apr 2020 22:50:53: #2 predicted fragment length is 127 bps INFO @ Wed, 15 Apr 2020 22:50:53: #2 alternative fragment length(s) may be 127 bps INFO @ Wed, 15 Apr 2020 22:50:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.05_model.r INFO @ Wed, 15 Apr 2020 22:50:53: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:50:53: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:50:55: 2000000 INFO @ Wed, 15 Apr 2020 22:50:58: 9000000 INFO @ Wed, 15 Apr 2020 22:51:00: 3000000 INFO @ Wed, 15 Apr 2020 22:51:03: 10000000 INFO @ Wed, 15 Apr 2020 22:51:05: 4000000 INFO @ Wed, 15 Apr 2020 22:51:07: 11000000 INFO @ Wed, 15 Apr 2020 22:51:09: 5000000 INFO @ Wed, 15 Apr 2020 22:51:12: 12000000 INFO @ Wed, 15 Apr 2020 22:51:14: 6000000 INFO @ Wed, 15 Apr 2020 22:51:17: 13000000 INFO @ Wed, 15 Apr 2020 22:51:19: 7000000 INFO @ Wed, 15 Apr 2020 22:51:21: 14000000 INFO @ Wed, 15 Apr 2020 22:51:22: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:51:22: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:51:22: #1 total tags in treatment: 14151931 INFO @ Wed, 15 Apr 2020 22:51:22: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:51:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:51:22: #1 tags after filtering in treatment: 14151931 INFO @ Wed, 15 Apr 2020 22:51:22: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:51:22: #1 finished! INFO @ Wed, 15 Apr 2020 22:51:22: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:51:22: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:51:23: #2 number of paired peaks: 1837 INFO @ Wed, 15 Apr 2020 22:51:23: start model_add_line... INFO @ Wed, 15 Apr 2020 22:51:23: start X-correlation... INFO @ Wed, 15 Apr 2020 22:51:23: end of X-cor INFO @ Wed, 15 Apr 2020 22:51:23: #2 finished! INFO @ Wed, 15 Apr 2020 22:51:23: #2 predicted fragment length is 127 bps INFO @ Wed, 15 Apr 2020 22:51:23: #2 alternative fragment length(s) may be 127 bps INFO @ Wed, 15 Apr 2020 22:51:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.10_model.r INFO @ Wed, 15 Apr 2020 22:51:23: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:51:23: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:51:24: 8000000 INFO @ Wed, 15 Apr 2020 22:51:24: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:51:28: 9000000 INFO @ Wed, 15 Apr 2020 22:51:33: 10000000 INFO @ Wed, 15 Apr 2020 22:51:38: 11000000 INFO @ Wed, 15 Apr 2020 22:51:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.05_peaks.xls INFO @ Wed, 15 Apr 2020 22:51:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.05_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:51:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.05_summits.bed INFO @ Wed, 15 Apr 2020 22:51:40: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (8218 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:51:42: 12000000 INFO @ Wed, 15 Apr 2020 22:51:47: 13000000 INFO @ Wed, 15 Apr 2020 22:51:51: 14000000 INFO @ Wed, 15 Apr 2020 22:51:52: #1 tag size is determined as 50 bps INFO @ Wed, 15 Apr 2020 22:51:52: #1 tag size = 50 INFO @ Wed, 15 Apr 2020 22:51:52: #1 total tags in treatment: 14151931 INFO @ Wed, 15 Apr 2020 22:51:52: #1 user defined the maximum tags... INFO @ Wed, 15 Apr 2020 22:51:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 15 Apr 2020 22:51:52: #1 tags after filtering in treatment: 14151931 INFO @ Wed, 15 Apr 2020 22:51:52: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 15 Apr 2020 22:51:52: #1 finished! INFO @ Wed, 15 Apr 2020 22:51:52: #2 Build Peak Model... INFO @ Wed, 15 Apr 2020 22:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 15 Apr 2020 22:51:53: #2 number of paired peaks: 1837 INFO @ Wed, 15 Apr 2020 22:51:53: start model_add_line... INFO @ Wed, 15 Apr 2020 22:51:54: start X-correlation... INFO @ Wed, 15 Apr 2020 22:51:54: end of X-cor INFO @ Wed, 15 Apr 2020 22:51:54: #2 finished! INFO @ Wed, 15 Apr 2020 22:51:54: #2 predicted fragment length is 127 bps INFO @ Wed, 15 Apr 2020 22:51:54: #2 alternative fragment length(s) may be 127 bps INFO @ Wed, 15 Apr 2020 22:51:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.20_model.r INFO @ Wed, 15 Apr 2020 22:51:54: #3 Call peaks... INFO @ Wed, 15 Apr 2020 22:51:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 15 Apr 2020 22:51:54: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.10_peaks.xls INFO @ Wed, 15 Apr 2020 22:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.10_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:52:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.10_summits.bed INFO @ Wed, 15 Apr 2020 22:52:09: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5273 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 15 Apr 2020 22:52:24: #3 Call peaks for each chromosome... INFO @ Wed, 15 Apr 2020 22:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.20_peaks.xls INFO @ Wed, 15 Apr 2020 22:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.20_peaks.narrowPeak INFO @ Wed, 15 Apr 2020 22:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX6720190/SRX6720190.20_summits.bed INFO @ Wed, 15 Apr 2020 22:52:38: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (2550 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。